In the plots below, “red” color represents read depth of sample and “blue” color represents read depth of wild-type ie ancestral strain with GFp.
# Rscript -e "library(knitr); knit('analyzing_for_CNVs.Rmd')" -p <pindel output .txt> -c <cnvnator output .txt> -l <lumpy output .txt> -r <read depth .txt file>
# This will out put a .md file and a directory named "figure" in your working directory
# To view this .md (which is similar to .html file genearted by Rmarkdown, make sure that the .html and corresponding "figures" folder is in the same directory
# Obtain read depth file for wild type before starting analysis
library(optparse)
library(knitr)## [1] "Mean Read Depth:"## [1] 45.4716## [1] "Deletion:Cnvnator"
## svtype chrom.1 start end size normRDsignal
## 6 deletion NC_001134.8 694501 695100 600 0.13
## 8 deletion NC_001135.5 56821 57360 540 0.15
## 9 deletion NC_001135.5 148621 151560 2940 0.01
## 10 deletion NC_001135.5 205561 206160 600 0.13
## 17 deletion NC_001139.9 2221 2580 360 0.02
## 18 deletion NC_001139.9 89281 90060 780 0.11
## 33 deletion NC_001143.9 15781 16320 540 0.07
## [1] 1
## svtype chrom.1 start end size normRDsignal
## 6 deletion NC_001134.8 694501 695100 600 0.13
## [1] 2
## svtype chrom.1 start end size normRDsignal
## 8 deletion NC_001135.5 56821 57360 540 0.15
## [1] 3
## svtype chrom.1 start end size normRDsignal
## 9 deletion NC_001135.5 148621 151560 2940 0.01
## [1] 4
## svtype chrom.1 start end size normRDsignal
## 10 deletion NC_001135.5 205561 206160 600 0.13
## [1] 5
## svtype chrom.1 start end size normRDsignal
## 17 deletion NC_001139.9 2221 2580 360 0.02
## [1] 6
## svtype chrom.1 start end size normRDsignal
## 18 deletion NC_001139.9 89281 90060 780 0.11
## [1] 7
## svtype chrom.1 start end size normRDsignal
## 33 deletion NC_001143.9 15781 16320 540 0.07
## [1] "Deletion:Lumpy"
## svtype chrom.1 start end size
## 1 DEL NC_001136.10 383817 384080 -263
## 10 DEL NC_001140.6 79753 80184 -431
## [1] 1
## svtype chrom.1 start end size
## 1 DEL NC_001136.10 383817 384080 -263
## [1] 2
## svtype chrom.1 start end size
## 10 DEL NC_001140.6 79753 80184 -431
## [1] "Deletion:Pindel"
## svtype chrom.1 start end size supporting.reads
## 169 D NC_001144.5 457786 466925 9138 28
## [1] 1
## svtype chrom.1 start end size supporting.reads
## 169 D NC_001144.5 457786 466925 9138 28
## [1] "Duplication:Cnvnator"
## svtype chrom.1 start end size normRDsignal
## 80 duplication NC_001133.9 162121 165900 3780 2.30
## 83 duplication NC_001134.8 222601 225000 2400 2.27
## 84 duplication NC_001134.8 259861 264120 4260 2.02
## 93 duplication NC_001136.10 527881 538380 10500 1.99
## 94 duplication NC_001136.10 647461 651120 3660 2.23
## 100 duplication NC_001136.10 987361 992340 4980 2.34
## 101 duplication NC_001136.10 1095841 1101540 5700 2.08
## 102 duplication NC_001136.10 1206961 1212240 5280 2.56
## 105 duplication NC_001137.3 443581 449040 5460 2.63
## 106 duplication NC_001137.3 493381 498360 4980 2.01
## 117 duplication NC_001139.9 535801 541560 5760 2.51
## 118 duplication NC_001139.9 563821 568200 4380 1.90
## 122 duplication NC_001140.6 40321 91080 50760 4.75
## 123 duplication NC_001140.6 212461 219660 7200 2.64
## 127 duplication NC_001140.6 544261 548460 4200 2.06
## 134 duplication NC_001142.9 111541 113160 1620 1.91
## 136 duplication NC_001142.9 472501 483840 11340 2.28
## 141 duplication NC_001143.9 650641 651540 900 2.78
## 144 duplication NC_001144.5 217801 220080 2280 2.30
## 146 duplication NC_001144.5 451441 472560 21120 31.59
## 147 duplication NC_001144.5 476341 481860 5520 2.37
## 149 duplication NC_001144.5 593401 596700 3300 2.57
## 150 duplication NC_001144.5 649981 655980 6000 2.22
## 154 duplication NC_001145.3 184261 190020 5760 2.24
## 155 duplication NC_001145.3 196621 202080 5460 2.54
## 160 duplication NC_001146.8 24661 26940 2280 1.86
## 162 duplication NC_001146.8 97321 100860 3540 2.37
## 165 duplication NC_001146.8 520201 524280 4080 1.98
## 170 duplication NC_001147.6 117961 123060 5100 2.75
## 171 duplication NC_001147.6 594901 599940 5040 2.13
## 175 duplication NC_001148.4 54961 61080 6120 2.22
## 181 duplication NC_001148.4 804841 810240 5400 2.16
## 182 duplication NC_001148.4 844501 856260 11760 2.13
## [1] 1
## svtype chrom.1 start end size normRDsignal
## 80 duplication NC_001133.9 162121 165900 3780 2.3
## [1] 2
## svtype chrom.1 start end size normRDsignal
## 83 duplication NC_001134.8 222601 225000 2400 2.27
## [1] 3
## svtype chrom.1 start end size normRDsignal
## 84 duplication NC_001134.8 259861 264120 4260 2.02
## [1] 4
## svtype chrom.1 start end size normRDsignal
## 93 duplication NC_001136.10 527881 538380 10500 1.99
## [1] 5
## svtype chrom.1 start end size normRDsignal
## 94 duplication NC_001136.10 647461 651120 3660 2.23
## [1] 6
## svtype chrom.1 start end size normRDsignal
## 100 duplication NC_001136.10 987361 992340 4980 2.34
## [1] 7
## svtype chrom.1 start end size normRDsignal
## 101 duplication NC_001136.10 1095841 1101540 5700 2.08
## [1] 8
## svtype chrom.1 start end size normRDsignal
## 102 duplication NC_001136.10 1206961 1212240 5280 2.56
## [1] 9
## svtype chrom.1 start end size normRDsignal
## 105 duplication NC_001137.3 443581 449040 5460 2.63
## [1] 10
## svtype chrom.1 start end size normRDsignal
## 106 duplication NC_001137.3 493381 498360 4980 2.01
## [1] 11
## svtype chrom.1 start end size normRDsignal
## 117 duplication NC_001139.9 535801 541560 5760 2.51
## [1] 12
## svtype chrom.1 start end size normRDsignal
## 118 duplication NC_001139.9 563821 568200 4380 1.9
## [1] 13
## svtype chrom.1 start end size normRDsignal
## 122 duplication NC_001140.6 40321 91080 50760 4.75
## [1] 14
## svtype chrom.1 start end size normRDsignal
## 123 duplication NC_001140.6 212461 219660 7200 2.64
## [1] 15
## svtype chrom.1 start end size normRDsignal
## 127 duplication NC_001140.6 544261 548460 4200 2.06
## [1] 16
## svtype chrom.1 start end size normRDsignal
## 134 duplication NC_001142.9 111541 113160 1620 1.91
## [1] 17
## svtype chrom.1 start end size normRDsignal
## 136 duplication NC_001142.9 472501 483840 11340 2.28
## [1] 18
## svtype chrom.1 start end size normRDsignal
## 141 duplication NC_001143.9 650641 651540 900 2.78
## [1] 19
## svtype chrom.1 start end size normRDsignal
## 144 duplication NC_001144.5 217801 220080 2280 2.3
## [1] 20
## svtype chrom.1 start end size normRDsignal
## 146 duplication NC_001144.5 451441 472560 21120 31.59
## [1] 21
## svtype chrom.1 start end size normRDsignal
## 147 duplication NC_001144.5 476341 481860 5520 2.37
## [1] 22
## svtype chrom.1 start end size normRDsignal
## 149 duplication NC_001144.5 593401 596700 3300 2.57
## [1] 23
## svtype chrom.1 start end size normRDsignal
## 150 duplication NC_001144.5 649981 655980 6000 2.22
## [1] 24
## svtype chrom.1 start end size normRDsignal
## 154 duplication NC_001145.3 184261 190020 5760 2.24
## [1] 25
## svtype chrom.1 start end size normRDsignal
## 155 duplication NC_001145.3 196621 202080 5460 2.54
## [1] 26
## svtype chrom.1 start end size normRDsignal
## 160 duplication NC_001146.8 24661 26940 2280 1.86
## [1] 27
## svtype chrom.1 start end size normRDsignal
## 162 duplication NC_001146.8 97321 100860 3540 2.37
## [1] 28
## svtype chrom.1 start end size normRDsignal
## 165 duplication NC_001146.8 520201 524280 4080 1.98
## [1] 29
## svtype chrom.1 start end size normRDsignal
## 170 duplication NC_001147.6 117961 123060 5100 2.75
## [1] 30
## svtype chrom.1 start end size normRDsignal
## 171 duplication NC_001147.6 594901 599940 5040 2.13
## [1] 31
## svtype chrom.1 start end size normRDsignal
## 175 duplication NC_001148.4 54961 61080 6120 2.22
## [1] 32
## svtype chrom.1 start end size normRDsignal
## 181 duplication NC_001148.4 804841 810240 5400 2.16
## [1] 33
## svtype chrom.1 start end size normRDsignal
## 182 duplication NC_001148.4 844501 856260 11760 2.13
## [1] "Duplication:Lumpy"
## svtype chrom.1 start end size
## 13 DUP NC_001145.3 908138 908616 478
## [1] 1
## svtype chrom.1 start end size
## 13 DUP NC_001145.3 908138 908616 478
## [1] "Duplication:Pindel"
## svtype chrom.1 start end size supporting.reads
## 278 TD NC_001144.5 457786 466923 9136 22
## 279 TD NC_001144.5 457786 466925 9138 14
## [1] 1
## svtype chrom.1 start end size supporting.reads
## 278 TD NC_001144.5 457786 466923 9136 22
## [1] 2
## svtype chrom.1 start end size supporting.reads
## 279 TD NC_001144.5 457786 466925 9138 14
pindel_del_filtered## svtype chrom.1 start end size supporting.reads
## 169 D NC_001144.5 457786 466925 9138 28cnv_del_filtered## svtype chrom.1 start end size normRDsignal
## 6 deletion NC_001134.8 694501 695100 600 0.13
## 8 deletion NC_001135.5 56821 57360 540 0.15
## 9 deletion NC_001135.5 148621 151560 2940 0.01
## 10 deletion NC_001135.5 205561 206160 600 0.13
## 17 deletion NC_001139.9 2221 2580 360 0.02
## 18 deletion NC_001139.9 89281 90060 780 0.11
## 33 deletion NC_001143.9 15781 16320 540 0.07lumpy_del_filtered## svtype chrom.1 start end size
## 1 DEL NC_001136.10 383817 384080 -263
## 10 DEL NC_001140.6 79753 80184 -431pindel_dup_filtered## svtype chrom.1 start end size supporting.reads
## 278 TD NC_001144.5 457786 466923 9136 22
## 279 TD NC_001144.5 457786 466925 9138 14cnv_dup_filtered## svtype chrom.1 start end size normRDsignal
## 80 duplication NC_001133.9 162121 165900 3780 2.30
## 83 duplication NC_001134.8 222601 225000 2400 2.27
## 84 duplication NC_001134.8 259861 264120 4260 2.02
## 93 duplication NC_001136.10 527881 538380 10500 1.99
## 94 duplication NC_001136.10 647461 651120 3660 2.23
## 100 duplication NC_001136.10 987361 992340 4980 2.34
## 101 duplication NC_001136.10 1095841 1101540 5700 2.08
## 102 duplication NC_001136.10 1206961 1212240 5280 2.56
## 105 duplication NC_001137.3 443581 449040 5460 2.63
## 106 duplication NC_001137.3 493381 498360 4980 2.01
## 117 duplication NC_001139.9 535801 541560 5760 2.51
## 118 duplication NC_001139.9 563821 568200 4380 1.90
## 122 duplication NC_001140.6 40321 91080 50760 4.75
## 123 duplication NC_001140.6 212461 219660 7200 2.64
## 127 duplication NC_001140.6 544261 548460 4200 2.06
## 134 duplication NC_001142.9 111541 113160 1620 1.91
## 136 duplication NC_001142.9 472501 483840 11340 2.28
## 141 duplication NC_001143.9 650641 651540 900 2.78
## 144 duplication NC_001144.5 217801 220080 2280 2.30
## 146 duplication NC_001144.5 451441 472560 21120 31.59
## 147 duplication NC_001144.5 476341 481860 5520 2.37
## 149 duplication NC_001144.5 593401 596700 3300 2.57
## 150 duplication NC_001144.5 649981 655980 6000 2.22
## 154 duplication NC_001145.3 184261 190020 5760 2.24
## 155 duplication NC_001145.3 196621 202080 5460 2.54
## 160 duplication NC_001146.8 24661 26940 2280 1.86
## 162 duplication NC_001146.8 97321 100860 3540 2.37
## 165 duplication NC_001146.8 520201 524280 4080 1.98
## 170 duplication NC_001147.6 117961 123060 5100 2.75
## 171 duplication NC_001147.6 594901 599940 5040 2.13
## 175 duplication NC_001148.4 54961 61080 6120 2.22
## 181 duplication NC_001148.4 804841 810240 5400 2.16
## 182 duplication NC_001148.4 844501 856260 11760 2.13lumpy_dup_filtered## svtype chrom.1 start end size
## 13 DUP NC_001145.3 908138 908616 478